Salk scientists add new bond to protein engineering toolbox

From left: Scientists Haiyan Ren, Lei Wang and Zheng Xiang

Proteins are the workhorses of cells,
adopting conformations that allow them to set
off chemical reactions, send signals and transport
materials. But when scientists are designing
a new drug, trying to visualize the processes
inside cells or probe how molecules interact
with each other, they can't always find a protein
that will do the job they want. Instead, they
often engineer their own novel proteins to use in
experiments, either from scratch or by altering
existing molecules.

As reported in Nature Methods, researchers
in the lab of Lei Wang have developed a new
tool for protein engineering: a way to add strong,
unbreakable bonds between two points in a
protein or between two proteins.

When a protein folds from a loose chain
of amino acid building blocks into its active
three-dimensional structure, bonds and
chemical interactions naturally form between
different parts of the chain to keep the structure
assembled. Most are relatively weak, driven by
the electrochemical charges of different amino
acids. Stronger bonds, called disulfide bridges,
occur between pairs of cysteines, one particular
amino acid. But for protein engineers, either
type of bond has had its own deficiencies. So
linking two parts of a protein in a predictable
and permanent way has been notoriously hard.

Wang and his team wanted to be able to
add strong, irreversible bonds—called covalent
bonds—to proteins to alter their shape, make
them more stable or attach them to one another.
So they began trying to create a new amino acid,
different from the 20 that exist naturally.

They created dozens of possible amino acids
and tested each one to see if it bound with just
the right strength. After a series of tests, they
settled on a newly created amino acid called
p-2-fluoroacetyl-phenylalanine, or Fact, then
designed three proteins using it in their
sequences. Tests of the proteins showed that
they formed a covalent bond with Fact.

"I think anyone who is working on proteins, or
anything related to proteins, could make use of
this new technology," says Wang. "It can provide
a novel way to control proteins or design proteins
to study basic biology."